Workflow Management Using Snakemake¶
In this webinar you’ll learn about snakemake, a workflow management system consisting of a text-based workflow specification language and a scalable execution environment. A workflow management system (WMS) is a piece of software that sets up, performs and monitors a defined sequence of computational tasks (i.e. “a workflow”). Snakemake is a WMS that was developed in the bioinformatics community, and as such it has some features that make it particularly well suited for creating reproducible and scalable data analyses.
- Snakemake syntax and basics
- Visualization and workflow management
- Example RNAseq workflow of MRSA
Downloads, access, and services¶
In order to complete this tutorial you will need access to the following services/software
Quick Launch Snakemake-VICE Jupyter lab app¶
OR search within Discovery Environment¶
Login to the Discovery Environment.
CLick on “Apps” tab in the Discovery Enviornment and search for “snakemake”.
Under “Analysis Name” leave the defaults or make any desired notes.
The app comes pre-loaded with required software required for performing RNAseq analysis.
Under “Resource Requirements” request resources as needed or leave for defaults
Click Launch Analysis. You will receive a notification that the job has been submitted and running in your notification tab.
You will be notified when the analysis has finished successfully.
6. Click on the “Analyses” button to display the dashboard of your analyses. Click on your anlaysis name to navigate to that analysis folder in your data store.
- Click here for the tutorial.
RNA-seq analysis of MRSA Workflow¶
- Clone RNAseq Snakemake tutorial repository
git clone https://github.com/NBISweden/workshop-reproducible-research.git cd workshop-reproducible-research/docker/ git checkout devel ls
- Generate rulegraph
snakemake --rulegraph | dot -Tpng > rulegraph_mrsa.png
- Dry-Run RNAseq Snakefile
- Run RNAseq Snakefile
snakemake --cores 8
Here we used the package snakemake-minimal. This is a slimmed down version that lack some features, in particular relating to cloud computing and interacting with remote providers such as Google Drive or Dropbox.
Other Workflow Managers¶
- CCTools offers Makeflow a workflow management system similar to Snakemake and also WorkQueue for scaling-up through Distributed Computing for customized and efficient utilization of resources. Read more here.
Additional information, help¶
- Snakemake Read The Docs
- Snakemake Tutorial
- Search for an answer: CyVerse Learning Center or CyVerse Wiki
- Contact CyVerse support by clicking the intercom button on the page.
Fix or improve this documentation